Job ID = 1295194 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,897,294 reads read : 11,897,294 reads written : 11,897,294 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:59 11897294 reads; of these: 11897294 (100.00%) were unpaired; of these: 1187399 (9.98%) aligned 0 times 8616402 (72.42%) aligned exactly 1 time 2093493 (17.60%) aligned >1 times 90.02% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1772125 / 10709895 = 0.1655 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 03 Jun 2019 12:40:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 12:40:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:40:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:40:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 12:40:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:40:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:40:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 12:40:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:40:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:40:14: 1000000 INFO @ Mon, 03 Jun 2019 12:40:19: 1000000 INFO @ Mon, 03 Jun 2019 12:40:19: 1000000 INFO @ Mon, 03 Jun 2019 12:40:24: 2000000 INFO @ Mon, 03 Jun 2019 12:40:33: 2000000 INFO @ Mon, 03 Jun 2019 12:40:33: 2000000 INFO @ Mon, 03 Jun 2019 12:40:34: 3000000 INFO @ Mon, 03 Jun 2019 12:40:45: 4000000 INFO @ Mon, 03 Jun 2019 12:40:46: 3000000 INFO @ Mon, 03 Jun 2019 12:40:47: 3000000 INFO @ Mon, 03 Jun 2019 12:40:54: 5000000 INFO @ Mon, 03 Jun 2019 12:40:57: 4000000 INFO @ Mon, 03 Jun 2019 12:40:59: 4000000 INFO @ Mon, 03 Jun 2019 12:41:03: 6000000 INFO @ Mon, 03 Jun 2019 12:41:08: 5000000 INFO @ Mon, 03 Jun 2019 12:41:11: 5000000 INFO @ Mon, 03 Jun 2019 12:41:12: 7000000 INFO @ Mon, 03 Jun 2019 12:41:19: 6000000 INFO @ Mon, 03 Jun 2019 12:41:21: 8000000 INFO @ Mon, 03 Jun 2019 12:41:23: 6000000 INFO @ Mon, 03 Jun 2019 12:41:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:41:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:41:29: #1 total tags in treatment: 8937770 INFO @ Mon, 03 Jun 2019 12:41:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:41:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 12:41:29: #1 tags after filtering in treatment: 8937770 INFO @ Mon, 03 Jun 2019 12:41:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:41:29: #1 finished! INFO @ Mon, 03 Jun 2019 12:41:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:41:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:41:30: 7000000 INFO @ Mon, 03 Jun 2019 12:41:30: #2 number of paired peaks: 293 WARNING @ Mon, 03 Jun 2019 12:41:30: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Mon, 03 Jun 2019 12:41:30: start model_add_line... INFO @ Mon, 03 Jun 2019 12:41:30: start X-correlation... INFO @ Mon, 03 Jun 2019 12:41:30: end of X-cor INFO @ Mon, 03 Jun 2019 12:41:30: #2 finished! INFO @ Mon, 03 Jun 2019 12:41:30: #2 predicted fragment length is 100 bps INFO @ Mon, 03 Jun 2019 12:41:30: #2 alternative fragment length(s) may be 83,100 bps INFO @ Mon, 03 Jun 2019 12:41:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.10_model.r WARNING @ Mon, 03 Jun 2019 12:41:30: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:41:30: #2 You may need to consider one of the other alternative d(s): 83,100 WARNING @ Mon, 03 Jun 2019 12:41:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 12:41:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:41:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:41:35: 7000000 INFO @ Mon, 03 Jun 2019 12:41:41: 8000000 INFO @ Mon, 03 Jun 2019 12:41:48: 8000000 INFO @ Mon, 03 Jun 2019 12:41:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:41:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:41:51: #1 total tags in treatment: 8937770 INFO @ Mon, 03 Jun 2019 12:41:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:41:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 12:41:52: #1 tags after filtering in treatment: 8937770 INFO @ Mon, 03 Jun 2019 12:41:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:41:52: #1 finished! INFO @ Mon, 03 Jun 2019 12:41:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:41:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:41:52: #2 number of paired peaks: 293 WARNING @ Mon, 03 Jun 2019 12:41:52: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Mon, 03 Jun 2019 12:41:52: start model_add_line... INFO @ Mon, 03 Jun 2019 12:41:52: start X-correlation... INFO @ Mon, 03 Jun 2019 12:41:52: end of X-cor INFO @ Mon, 03 Jun 2019 12:41:52: #2 finished! INFO @ Mon, 03 Jun 2019 12:41:52: #2 predicted fragment length is 100 bps INFO @ Mon, 03 Jun 2019 12:41:52: #2 alternative fragment length(s) may be 83,100 bps INFO @ Mon, 03 Jun 2019 12:41:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.20_model.r WARNING @ Mon, 03 Jun 2019 12:41:52: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:41:52: #2 You may need to consider one of the other alternative d(s): 83,100 WARNING @ Mon, 03 Jun 2019 12:41:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 12:41:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:41:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:41:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:41:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:41:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:41:58: #1 total tags in treatment: 8937770 INFO @ Mon, 03 Jun 2019 12:41:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:41:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 12:41:58: #1 tags after filtering in treatment: 8937770 INFO @ Mon, 03 Jun 2019 12:41:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:41:58: #1 finished! INFO @ Mon, 03 Jun 2019 12:41:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:41:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:41:59: #2 number of paired peaks: 293 WARNING @ Mon, 03 Jun 2019 12:41:59: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Mon, 03 Jun 2019 12:41:59: start model_add_line... INFO @ Mon, 03 Jun 2019 12:41:59: start X-correlation... INFO @ Mon, 03 Jun 2019 12:41:59: end of X-cor INFO @ Mon, 03 Jun 2019 12:41:59: #2 finished! INFO @ Mon, 03 Jun 2019 12:41:59: #2 predicted fragment length is 100 bps INFO @ Mon, 03 Jun 2019 12:41:59: #2 alternative fragment length(s) may be 83,100 bps INFO @ Mon, 03 Jun 2019 12:41:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.05_model.r WARNING @ Mon, 03 Jun 2019 12:41:59: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:41:59: #2 You may need to consider one of the other alternative d(s): 83,100 WARNING @ Mon, 03 Jun 2019 12:41:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 12:41:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:41:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:42:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:42:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:42:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.10_summits.bed INFO @ Mon, 03 Jun 2019 12:42:09: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (848 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:42:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:42:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:42:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:42:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:42:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.20_summits.bed INFO @ Mon, 03 Jun 2019 12:42:31: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (557 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:42:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:42:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:42:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331379/SRX331379.05_summits.bed INFO @ Mon, 03 Jun 2019 12:42:38: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1163 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。